Structure of PDB 4ynb Chain A Binding Site BS01

Receptor Information
>4ynb Chain A (length=230) Species: 85963 (Helicobacter pylori J99) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYS
KIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQH
DVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASG
DQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNA
DEKAGMSFDEFLEKSAHTSAKFLKSMVDEL
Ligand information
Ligand ID4EH
InChIInChI=1S/C16H19N7OS/c17-16-15-14(21-9-22-16)10(3-20-15)5-23-6-11(12(24)7-23)8-25-13-4-18-1-2-19-13/h1-4,9,11-12,20,24H,5-8H2,(H2,17,21,22)/t11-,12+/m1/s1
InChIKeyUMOBRIXOOIFSTP-NEPJUHHUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSc4cnccn4)C3)c[nH]c12
CACTVS 3.385Nc1ncnc2c(CN3C[CH](O)[CH](CSc4cnccn4)C3)c[nH]c12
OpenEye OEToolkits 1.9.2c1cnc(cn1)SC[C@H]2CN(C[C@@H]2O)Cc3c[nH]c4c3ncnc4N
OpenEye OEToolkits 1.9.2c1cnc(cn1)SCC2CN(CC2O)Cc3c[nH]c4c3ncnc4N
ACDLabs 12.01OC3CN(Cc1cnc2c1ncnc2N)CC3CSc4cnccn4
FormulaC16 H19 N7 O S
Name(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(pyrazin-2-ylsulfanyl)methyl]pyrrolidin-3-ol
ChEMBL
DrugBank
ZINCZINC000143833774
PDB chain4ynb Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ynb New Antibiotic Candidates against Helicobacter pylori.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		M11 I53 V79 A80 G81 F154 V155 V173 E174 M175 E176 D199 F209
Binding residue
(residue number reindexed from 1)		M10 I52 V78 A79 G80 F153 V154 V172 E173 M174 E175 D198 F208
Annotation score1
Binding affinityMOAD: Ki=0.043nM
PDBbind-CN: -logKd/Ki=10.37,Ki=0.043nM
Enzymatic activity
Enzyme Commision number 3.2.2.30: aminodeoxyfutalosine nucleosidase.
3.2.2.9: adenosylhomocysteine nucleosidase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008782 adenosylhomocysteine nucleosidase activity
GO:0008930 methylthioadenosine nucleosidase activity
GO:0016787 hydrolase activity
GO:0102246 6-amino-6-deoxyfutalosine hydrolase activity
Biological Process
GO:0009086 methionine biosynthetic process
GO:0009116 nucleoside metabolic process
GO:0009164 nucleoside catabolic process
GO:0009234 menaquinone biosynthetic process
GO:0019284 L-methionine salvage from S-adenosylmethionine
GO:0019509 L-methionine salvage from methylthioadenosine
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ynb, PDBe:4ynb, PDBj:4ynb
PDBsum4ynb
PubMed26494017
UniProtQ9ZMY2|MQMTN_HELPJ Aminodeoxyfutalosine nucleosidase (Gene Name=mtnN)

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